I would think it would be a easy task to create a small program you could run that would fix this. What I mean is, you could alter your shortcut to run a small program instead of the actual program, passing the actual program command line to that small program. The small program would turn off screen saver and other things (liker power saving options), start and wait for the actual program, then turn back on the things it disabled.
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Lasse V. KarlsenJul 20 '09 at 10:06

Please add this as an answer, not a comment.
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Stijn SandersJul 20 '09 at 16:00